University of Minnesota
MICaB Graduate Program
http://micab.umn.edu
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MICaB Course Information

Curriculum Written Proposition & Oral Examination
Registration Assign/Update Doctoral Final Committee
Financial Assistance Thesis - Preparation and submission
Teaching Seminars and Journal Clubs
Graduate Degree Plan Fellowship Opportunities
 

 


Curriculum

MICaB - Major Requirements


A student must earn between 48 and 72 credits to obtain a doctoral degree at the University of Minnesota. At least 24 must be course credits and at least 24 must be thesis credits

Course Credits
The course credits consist of required and elective credits. Both Ph.D. and M.D./Ph.D. MICaB students are required to take: 1) one core course (in the student’s track), 2) one focus area course (see below), and 3) MICA 8012 (to prepare for the preliminary examinations). Ph.D. students in their first year are also required to register 1 credit each semester for MICA 8094 (Research in MICaB; lab rotations).

Thesis Credits
The Graduate School requires students earn at least 24 doctoral thesis (research-related) credits. MICaB permits students to register for these credits (MICA 8888) beginning their first semester. The course and thesis credits total 48, which is the minimal requirement to earn a doctoral degree at the University of Minnesota.

All MICaB students are required to take the following:
Course
Title
Credits/Semester (Fall, Spring)
MICa 8012 Integrated Topics in MICaB 2 cr F of 2nd year
MICa 8094 Research in MICaB (lab rotations) 1 cr F/S
MICa 8910 (2 years) Faculty Seminar 0 cr F/S
MICa 8920 (2 years) Student Seminar 0 cr F/S
MICa 5000 Practicum: Teaching 0 cr F/S
  Responsible Conduct of Research, Part 1 Fall, 1st year
  Responsible Conduct of Research, Part 2 Fall, 1st year
  MICaB Ethics Workshop Spring, 1st year
 

Major Course Requirements:
Students are encouraged to take all three of the MICa core courses listed below; however only one course is required.
One of the following core courses in Year 1:

MICa 8002 Structure, Function & Genetics 4 F
MICa 8003 Immunity and Immunopathobiology 4 F
MICa 8004 Biology of Cancer 4 S


plus:

One Focus Area science course (5000-level or higher, minimum 3 credits) in Year 1 or 2. The course can be any university graduate-level science course related to the student’s area of interest.  A student may use MICa 8002, MICa 8003 or MICa 8004 as a focus area course. U of M-TC courses: https://webapps-prd.oit.umn.edu/courses/designators.jsp?campus=UMNTC

MICaB Focus Areas:

  • Microbiology / Immunology / Cancer Biology
  • Microbiology / Immunology
  • Immunology / Cancer Biology
  • Microbiology / Cancer Biology
  • Microbiology
  • Immunology
  • Cancer Biology


Focus Area Selection:
An appropriate focus area will be chosen by the student in their first year, most likely after PhD advisor selection.  The student, along with their advisor, will discuss the interests and academic needs of the student and determine which major course will fulfill the focus area requirement. The  Focus Area will also influence the makeup of the student’s preliminary examination committee since that examination will test the student on the fundamental and key concepts in the student’s Focus Area.

In the fall semester of their first year, students must take the University ethics training: Responsible Conduct of Research (RCR), Part 1 (a 3-hour session; sign up at  http://www.research.umn.edu/first/CourseSchedReg.htm)  and Part 2 (taken online) in their first semester.  In spring semester, first-year students are also required to attend a MICaB-sponsored ethics workshop.

MICa 8012 must be taken in the fall of Year 2 and the other one MICa course (chosen from MICa 8002, 8003, and 8004) you take for major credit must be taken in Year 1.

 

Please review the MICaB website at http://www.micab.umn.edu/current/courses.html for a list of recommended supporting courses. 

4000-level courses.  Only one 4000-level course may be applied toward program credits.

3000-level courses CANNOT be applied toward the 24 course credit requirement.

Preparing Future Faculty.  Preparing Future Faculty (PFF) is a program co-sponsored by the Graduate School and the Office of Human Resources to provide graduate students and postdoctoral fellows with special teaching and learning opportunities in higher education.  More information about the program, PFF courses, and mentoring and teaching opportunities is available on the PFF web site (http://www1.umn.edu/ohr/teachlearn/pff/).  Although MICaB students may take both PFF courses (GRAD 8101 and GRAD 8200), ONLY 1 may be applied to the student’s 24 credit requirements.

GRAD 5102.  MICaB students who are non-native speakers of English may take GRAD 5102, Preparation for University Teaching for Nonnative English Speakers, to improve written and oral communication skills.  However, this course may NOT be applied to the student’s course credit requirements.

Academic Performance Expectations.  The MICaB program requires that all course work taken by MICaB students be graded using the A-F system. Students are expected to receive a grade of B or better in each of these courses. Any grade lower than a C is unacceptable. Students must maintain a grade point average of 3.0 in the major course requirements. Students who do not maintain a grade point average of 3.0 will be excused from the program.

Class Schedule.  The class schedule is online at http://onestop2.umn.edu/courseinfo/classschedule_selectsubject.jsp?institution=UMNTC.

Recommendations for supporting credits:

Fall Semester

BioC 8001. Biomoleculars and Enzymology. Doug Ohlendorf and David Bernlohr, 10:10-11:00, MWF (3 cr).

BioC 8002. Molecular Biology and Reg Biol Processes. Jeongsik Yong 8:15-9:30 MW (3 cr)
Structure/stability of nucleic acids, genome organization. Chromosome mchanics, including DNA replication, recombination, and transposable elements. Mechanism/regulation of gene expression, including transcription, processing, and translation. Genetic/enzymatic controls. Cell cycle controls. Regulation of development.

BioC 5361. Microbial Genomics and Bioinformatics, Larry Wackett and Arkady Khodursky, (3 cr), 10:15-11:30 T TH. Introduction to genomics with an emphasis on developments in microbial genomics. The topics to be covered are sequencing methodologies, sequence analysis, genomics databases, information theory and statistics, protein and DNA structure, proteomics and the genomes of model microbes

ChEn 8995. Systems Analysis of Biological Processes. Wei-Shou Hu (1-4 cr) 2:30-4:30 F
Designed for graduate students from life sciences, chemical and physical sciences and engineering with interest in quantitative analysis of biological systems.

GCD 6103 Human Histology Jan Norrander (max crs 8.0; 1 repeats allowed; P-N or Audit; Enrolled as medical or dental student or instr consent) 10:10am-12:05pm MW, PWB 2-470, TCEASTBANK 15401
002 LAB 3-8 cr, med students only, 200 of 200 seats open Meets with: GCD 8103 section 002
003 LAB 5 cr, dent students only, 80 of 80 seats open Meets with: GCD 8103 section 003

GCD 8131. Advanced Molecular Genetics and Genomics. David Greenstein, Nik Somia, Ran Blekhman. 11:15-12:05 MWF (3 cr)
Literature-based course covering modern genetic analysis, including mutant screens, characterization of multiple alleles, gene mapping and cloning, genome sequencing, intergenic interactions, transposable elements, genetic mosaics, and molecular mechanisms of recombination

GCD 8151. Cellular Biochemistry and Cell Biologoy. Margaret Titus, Daniel Schmidt, Deanna Koepp, Sean Connor, Gant Luxton, 9:45-11:00 TTh (3 cr).
Eukaryotic systems with emphasis on structure, function, and chemistry of cell organelles; selected specialized cells. Membranes, secretion, trafficking, cytoskeleton, cell motility, cell cycle, nucleus, and compartmentalization.

SCB 8181. Stem Cell Biology. Susan Keirstead (3 cr; prereq [[4034 or 8121 or BIOC 8002], [4161 or 8161]] or instr consent), 3 credits, 3 sessions/week MCB 2-122. This course, formerly GCD 8181, has evolved over recent years and is now well established. It is designed for first year graduate students but can also be taken by later years. Because of its interdisciplinary character it is appropriate as an elective for a wide range of graduate programs in the Academic Health Center, the Colleges of Biological Sciences, Agriculture and Veterinary Medicine, and the Institute of Technology.

MICa 8010 Microbial Pathogenesis (A-F only; MICa grad student or instr) LEC 08:30-09:45 WF, Southern, Peter , 3 cr Molecular mechanisms of bacterial/viral pathogenesis. Strategies of disease causation/interaction with host, regulation of virulence factors, mechanism of virulence factor transmission to other microbes. Offered every other year, even years.

MICa 8371 Mucosal Immunobiology: (A-F only; Credit will not be granted if credit has been received for: MVB 8371, OBIO 8371), LEC 3:00-4:30 MW (3 credits), Herzberg, Mark. Offered every other year, odd years.


Spring Semester

GCD 8073. Advanced Human Genetics and Genomics. Heather Zierhut, 1:00-2:15 MW (3 cr)
Application of molecular, biochemical, chromosomal, and population genetics to human variation and disease. Abnormal chromosome number and structure; abnormal enzyme, structural protein, receptor and transport; analysis of inheritance patterns; behavioral genetics; genetic basis of common disease. Current research articles in human genetics.

GCD 8161. Cell Biology and Development. Laura Gammill, Margaret Titus, Yasu Kawakami, Ann Rougvie, Tom Neufeld, Michael O'Connor, 9:45-11:00 TTh (3 cr)
Current concepts of and experimental approaches taken to understand basic mechanisms of development. Model organisms. Embryology, cell fate determination, differentiation, pattern formation, polarity, cell migration, and cell interactions. Analysis of original research articles.

GCD 8008. Mammalian Gene Transfer. Scott McIvor 9:05-11:00, T(2 cr). Current gene transfer technology and applications of genetic modifications in animals, particularly transgenic animals and human gene therapy.

MICa 8009. Biochemical Aspects of Normal and Abnormal Cell Growth and Cell Death. Khalil Ahmed (2 cr; 8004 or [BioC 3021, Biol 4004] or #) 03:35pm-05:30pm F Aspects of mechanisms involved in growth control at level of nuclear function. Neoplasia in hormonal cancers (such as prostate cancer) and role of protein phosphorylation in normal and abnormal growth. Mechanisms of cell death via apoptosis and its implications in normal and abnormal proliferation.

MICa 8011 Topics in Immunology: (A-F only; SP - MICA 8003 or instr consent) LEC 1:30-2:45 Tu, T, TCEASTBANK, Steve Jameson, Colloquium format. In-depth reading, discussion

MICa 8013. Translational Cancer Research. David Potter and David Largaespada. (2 cr, prerequisites: MICa 8012, MICa 8004 or instructor's consent). Tu 8:00 - 8:50 am. The goals of the course are to expose Ph.D. students to clinical issues in cancer research and to discuss translational research projects as they pertain to a variety of cancers.  In particular, we will present cutting-edge concepts in cancer treatment including immunotherapy, anti-angiogenesis, small molecules, pharmacogenomics, and cancer prevention in high-risk populations.  We will emphasize exciting and controversial topics in treatment of a variety of important cancers.

MICa 8014. Small RNA Biology. Subbaya Subramanian. (2 credits, Thurs, 1:00-2:30) Small RNAs especially microRNAs have emerged as a major regulators of gene expression. Recently, microRNAs have been demonstrated for their potential use in diagnosis and prognosis of various disease conditions including cancers. Recent advances in understanding the biology of miRNA biogenesis and function have contributed to a greater extent in deciphering the molecular mechanism(s) of disease development and progression. The goals of the course are to expose the PhD students to the biology of small RNAs and their role in health and disease. Further, the course will highlight the recent advances in the research methodologies and next generation approaches to understand the small RNA function and gene regulatory networks. 

BioC 8216. Signal Transduction and Gene Expression. Do-Hyung Kim (4 cr; BioC 8002 or #) 2:30-4:25 TTh
Cell signaling, metabolic regulation in development. Procaryotic/eucaryotic systems used as models for discussion. Literature-based course.

BioC 5352. Microbial Biochemistry and Biotechnology: Proteins . Michael Flickinger. (3 cr) 1:55-2:45 pm MWF. Offered every other odd years. BioC 5353 is offered even years.

 

For students interested in genomics:

Spring Semester
PHCL 5111. Pharmacogenomics
. Campbell & Pei (3.0 cr; SP-Grad student or #; A-F only) 3:30-4:30 M, 2:00-4:00 W
Human genetic variation, its implications. Functional genomics, pharmacogenomics, toxicogenomics, proteomics. Interactive, discussion-based course.

GCD 8920. Computational Genomics. Ran Blekhman, Frank Albert, 8:15-9:30 TTh (2 cr).

Fall Semester
BioC 5361. Microbial Genomics and Bioinformatics. Larry Wackett (3.0 cr; SP-College-level courses in [organic chemistry, biochemistry, microbiology]) 10:15am-11:30am TTh
Introduction to genomics. Emphasizes microbial genomics. Sequencing methods, sequence analysis, genomics databases, genome mapping, prokaryotic horizontal gene transfer, genomics in biotechnology, intellectual property issues.

CSci 5481 Computational Techniques of Genomics. George Karypis (CSci 4041 or instr consent)2:30-3:45 pm, TTh

Search for classes at:

https://www.myu.umn.edu/psp/psprd/EMPLOYEE/CAMP/c/SA_LEARNER_SERVICES.CLASS_SEARCH.GBL


Registration

Registration is completed online at http://onestop.umn.edu/onestop/registration.html.  ALL Graduate School students are required to register in the Graduate School every fall and spring term in order to maintain active status.

In years 1 and 2, all students should register for a total of 14 course and thesis (MICa 8888) credits per semester. The number of thesis credits to register for each semester equals 14 minus the number of course credits taken that semester. 

Students scheduled to complete their teaching requirement should register for MICa 5000 even though there is no credit associated with the TA requirement.

Thesis Credits.  The Graduate School requires students earn at least 24 doctoral thesis (research-related credits. MICaB permits students to register for these credits (MICa 8888) beginning their first semester. The rationale is to decrease the time it takes to accumulate at least 24 course plus 24 thesis credits. The course and thesis credits total 48, which is the minimal requirement to earn a doctoral degree at the University of Minnesota. Once these 48 credits are earned, tuition fees drop dramatically.

Students who have completed the 24 course credits and 24 thesis credits should register for MICa 8444 1 FTE only and complete the one-credit registration request (available from the MICaB Program Coordinator).  The one-credit registration request must be completed every semester of enrollment. 

Summer Registration. Students should not register for summer session unless the student is a NSF fellow or needs to complete the 24 MICa 8888 thesis credit minimum in order to graduate the following fall. Students who register for summer session must complete the "Summer Request for Tuition Benefits" form and submit it to the Graduate Assistant Office (200 Donhowe) and a copy to the student's departmental payroll office.

Financial Assistance

Students are provided with stipend (currently $26,500 for years 1 and 2 and $27,500 for years 3+ (or when course and thesis credits are completed and successfully pass oral preliminary examination) and fringe benefit support for their entire training period as long as they make satisfactory progress. Support is awarded on a semester basis. First-year students are supported by Research Assistantships from the MICaB program. Funds for this purpose come from the Department of Microbiology, the Center for Immunology, the Masonic Cancer Center, the Medical School, Graduate School Block Grants, or Graduate School Fellowships for New Students. Presently, full tuition remission and eligibility for the Graduate Assistant Health-Care Plan accompanies these assistantships. Students pay student services fees. First-year student assistantships extend through the entire rotation period (up to 30 weeks). Once a first-year student selects an advisor, his or her support must come from that advisor via one or more of the following sources:

 

  1. Research Assistantships from Federal and Non-Federal Research Grants awarded to the advisor. Full tuition remission and eligibility for the Graduate Assistant Health-Care Plan accompanies the assistantship. Students pay student services fees.
  2. USPHS Institutional Research Service Traineeships (NIH Training Grants). These carry a stipend set by the USPHS. Tuition and fees are paid by the Training Grant. These stipend awards are available to students studying with a training grant faculty member and are generally awarded only after the first year of study. MICaB program faculty currently participate in NIH training grants in immunology, biotechnology, chemistry and biology, infectious diseases, and cancer biology.
  3. National Fellowships. We encourage incoming students to apply for individual awards from the Howard Hughes Medical Institution, the National Science Foundation and the National Institutes of Health prior to matriculation. Students awarded a fellowship are given a 10% stipend increase.
  4. Fellowships for under-represented minority students. Such fellowships are available from the Graduate School, the National Institutes of Health, the National Science Foundation and other sources.
  5. University Fellowships. These vary in amount and duration according to the source of the fellowship. Some require nomination by the CGS and are competitive. Details are available in the Graduate School Fellowship Office. Subject to the availability of funds, financial support of the student who is progressing satisfactorily in the graduate program is renewed each quarter for up to five years. Financial support will be terminated if satisfactory progress is not made. Support beyond the fifth year must be approved by the CGS, and will only be considered if there are extenuating circumstances.
  6. American Society for Microbiology (ASM). The Office of Education and Training of the ASM offers career information and fellowship opportunities in the biological/microbiological sciences at the undergraduate, graduate, and post doctoral level.

Teaching

An essential aspect of advanced study in biology is the experience gained in teaching and in preparation for laboratory courses. For this reason, the MICaB program requires that each Ph.D. student assist in laboratory teaching for one semester and serve as a grader for one semester during their tenure in the program.  Typical teaching duties include assisting students in a “wet lab”, preparing reagents and equipment for student use, grading notebooks and examinations, and conducting tutorial and review sessions. 

Teaching requirements are typically fulfilled beginning in the fall semester of the second year in the MICaB program.  The MICaB Program Coordinator will notify students by E-mail prior to the start of the fall semester regarding the available teaching opportunities.  Students should respond promptly to this E-mail with specific preferences and any obligations or commitments that may conflict with teaching in any given semester.  The MICaB program will make every effort to accommodate specific preferences, but this is not guaranteed.

Information for MICaB students who are Nonnative English Speakers.  University of Minnesota policy requires that all nonnative English speaking teaching assistants take the SPEAK test or provide official documentation of their score on the Test of Spoken English (TSE).  University of Minnesota policy considers a nonnative speaker to be a person who grew up in a home where the language was other than English.  This applies to US citizens and to those who have degrees from institutions in the United States or countries where English is the medium of instruction. 

The MICaB program recommends that all students who are nonnative English speakers take the SPEAK test during their first year in the program.  Students must obtain a minimum score of 50 on the SPEAK test in order to be able to complete their teaching requirements in the MICaB program.

Students can register for the SPEAK test in person at Room 312 Science Classroom Building or by phone at 612-625-3041.  Additional information on the SPEAK test is available at http://www1.umn.edu/ohr/teachlearn/nonnative/speak/index.html

Additional resources for Nonnative English speakers engaged in teaching are available at the Center for Teaching and Learning Services (http://www1.umn.edu/ohr/teachlearn/nonnative/index.html) and the International TA Program

Teaching Resources.  The Center for Educational Innovation provides resources for a successful teaching experience. These resources include a Teaching Enrichment Series and Online Tutorials

For students seeking help in writing:

Center for Writing: http://writing.umn.edu/

The following courses are also available for students who are non-native speakers of English:

ENGC 5051 - Graduate Research Writing Practice for Non-native Speakers of English
(3.0 cr; Prereq-Grad student; fall, spring, summer, every year)
Graduate-level writing techniques/formats for summaries, critiques, research, and abstracts. Persuasion, documentation, structure, grammar, vocabulary, field-specific requirements. Writing through several drafts, using mentor in specific field of study. Revising/editing to meet graduate standards. Discussions.

ENGC 5052 - Graduate Research Presentations and Conference Writing for Non-native Speakers of English
(3.0 cr; Prereq-[Grad student, non-native speaker of English] or #; fall, spring, every year)
Practice in writing/presenting graduate-level research for conferences or professional seminars. Delivery of professional academic presentations to U.S. audiences. Conference abstract, paper, and poster presentation. Communication in research process. Students select topics from their own research/studies. Format, style, transitions, topic narrowing, non-verbal presentation skills.

NOTE: ENGC 5051 and ENGC 5052 may NOT be applied to a student's supporting program.

 

Written Proposition and Oral Preliminary Examination Guidelines pdf

Doctoral Final Examining Committee

Following passage of the preliminary oral examination, students must file online the Doctoral Final Examining Committee.

Thesis - Preparation

Students nearing the completion of their thesis research should raise the possibility of finishing the program with their thesis committee at their annual progress review meeting. If the thesis committee agrees that the student has enough results to form a defensible thesis, the student begins writing the thesis. Students should read the guidelines for preparing a thesis which are available online from the Graduate School.

After the thesis is completed and the advisor is satisfied with the draft, the student submits a typed copy to the thesis reviewers and other members of the examining committee. The committee members must be given adequate time (one month) to confer with the candidate on the content of the thesis. After this draft has been tentatively approved, the student prepares the final thesis and resubmits it to all members of the thesis committee. Acceptance of the thesis indicates that the thesis has been corrected in proper response to the comments of the committee members. The thesis reviewers then sign a Graduate School form certifying that the thesis is ready for oral defense.

The candidate should contact the MICaB office for room arrangements and to send out announcements. The candidate then presents his/her thesis in a public seminar with the examining committee present. The seminar constitutes the final oral examination, and is followed by a short meeting of the examining committee, who must sign a Graduate School form indicating the results of the final oral examination. A member of the examining committee other than the advisor chairs the final oral examination. All faculty and students are urged to attend the final oral examination.

Thesis - Submission

The Graduate School requires all students submit the thesis online. The graduate school also requires a hard copy of the signature page, title page and deposit agreement (submitted to 160 Williamson Hall). Doctoral students are also required to submit an electronic University of Minnesota Survey of Earned Doctorates (sign in with your UM internet ID).

Students may copy their Ph.D. or M.S. theses on a departmental copier. The MICaB Program will pick up the copying charges, but students must supply their own paper. Thesis binding is the student's responsibility.

Seminars and Journal Clubs

SEMINARS

MICaB Invited Speaker Seminar Series.  The MICaB Invited Speaker Seminar Series features research presentations from scientists from other institutions who have been invited to the University of Minnesota by MICaB faculty.  The seminar is held on Mondays at Noon during the academic year (see http://www.micab.umn.edu/news/invitedsemseries.html for the room and seminar schedule).  Students and postdocs have lunch with the seminar speaker after the seminar.  Students are also encouraged to attend a “Beer and Science” session on Monday afternoons for an in-depth discussion with the seminar speaker.  The student who chooses to attend is opening the network to future success and development. 

Masonic Cancer Center Seminar Series.  The Cancer Center Seminar Series features cancer-related research presentations from local and external scientists.  The seminar is held on Tuesdays at Noon during the academic year in Room 450 MCRB.  See http://www.cancer.umn.edu/education-and-training-opportunities/cancer-center-seminars/index.htm for the current seminar schedule. 

MICaB Student Seminar Series.  The MICaB Student Seminar Series features research presentations by current MICaB students.  The seminar is held on Thursdays at Noon during the academic year (see http://www.micab.umn.edu/news/studentsemseries.html for the room and seminar schedule).

MICaB Ph.D. students are required to give a presentation in the MICaB Student Seminar Series during their second and fourth years in the program.  MICaB M.D./Ph.D. students are required to give a presentation in the MICaB Student Seminar Series during their first and third years in the program.  The first seminar will be a 20-25 minute presentation, while the second seminar will be a 40-45 minute presentation.  Three MICaB faculty members (one from each track) will evaluate the seminar presentation.  Following the seminar, each of these faculty members will meet with the student to provide feedback to help improve the student’s seminar presentation skills.

Seminar attendance requirements.  All students in the MICaB program are expected to attend the MICaB Student Seminar Series and either the MICaB Invited Speaker Series or the Cancer Center Seminar Series every week. 

During the first two years in the MICaB program, students must attend both semesters (Fall and Spring) for MICa 8910 (Faculty seminar) AND MICa 8920 (Student seminar). 

Student-invited seminar speakers.  Each year, students in the MICaB program invite distinguished scientists to visit and present their latest research to the MICaB program.  There are three student-invited seminar speakers, one for each track.  These speakers are nominated and selected by the students, and a student host coordinates the visit.  The MICaB student representatives are responsible for soliciting nominations, handling the voting process, and identifying student hosts for the speakers.

JOURNAL CLUBS AND DATA CLUBS

Journal clubs and data clubs provide important opportunities for students to improve their communication skills, stay current on the latest research, and obtain feedback on their research.

Students in the MICaB program are required to make a minimum of one presentation per year of a peer-reviewed publication in a journal club focused on research relevant to the student’s thesis research.  The following journal clubs hold regular meetings:

Students should also give regular “research-in-progress” presentations at data club meetings, such as the Immunology Supergroup meeting or the Cancer Biology Research Club meeting.